The first genetic linkage map for Fraxinus pennsylvanica and syntenic relationships with four related species.
Identifieur interne : 000678 ( Main/Exploration ); précédent : 000677; suivant : 000679The first genetic linkage map for Fraxinus pennsylvanica and syntenic relationships with four related species.
Auteurs : Di Wu [États-Unis] ; Jennifer Koch [États-Unis] ; Mark Coggeshall [États-Unis] ; John Carlson [États-Unis]Source :
- Plant molecular biology [ 1573-5028 ] ; 2019.
Descripteurs français
- KwdFr :
- Animaux (MeSH), Café (génétique), Cartographie chromosomique (MeSH), Coléoptères (MeSH), Fraxinus (génétique), Fréquence d'allèle (MeSH), Génome végétal (génétique), Liaison génétique (MeSH), Lycopersicon esculentum (génétique), Polymorphisme de nucléotide simple (génétique), Répétitions microsatellites (génétique), Synténie (génétique), Techniques de génotypage (MeSH).
- MESH :
English descriptors
- KwdEn :
- Animals (MeSH), Chromosome Mapping (MeSH), Coffee (genetics), Coleoptera (MeSH), Fraxinus (genetics), Gene Frequency (MeSH), Genetic Linkage (MeSH), Genome, Plant (genetics), Genotyping Techniques (MeSH), Lycopersicon esculentum (genetics), Microsatellite Repeats (genetics), Polymorphism, Single Nucleotide (genetics), Synteny (genetics).
- MESH :
- chemical , genetics : Coffee.
- genetics : Fraxinus, Genome, Plant, Lycopersicon esculentum, Microsatellite Repeats, Polymorphism, Single Nucleotide, Synteny.
- Animals, Chromosome Mapping, Coleoptera, Gene Frequency, Genetic Linkage, Genotyping Techniques.
Abstract
KEY MESSAGE
The genetic linkage map for green ash (Fraxinus pennsylvanica) contains 1201 DNA markers in 23 linkage groups spanning 2008.87cM. The green ash map shows stronger synteny with coffee than tomato. Green ash (Fraxinus pennsylvanica) is an outcrossing, diploid (2n = 46) hardwood tree species, native to North America. Native ash species in North America are being threatened by the rapid spread of the emerald ash borer (EAB, Agrilus planipennis), an invasive pest from Asia. Green ash, the most widely distributed ash species, is severely affected by EAB infestation, yet few genomic resources for genetic studies and improvement of green ash are available. In this study, a total of 5712 high quality single nucleotide polymorphisms (SNPs) were discovered using a minimum allele frequency of 1% across the entire genome through genotyping-by-sequencing. We also screened hundreds of genomic- and EST-based microsatellite markers (SSRs) from previous de novo assemblies (Staton et al., PLoS ONE 10:e0145031, 2015; Lane et al., BMC Genom 17:702, 2016). A first genetic linkage map of green ash was constructed from 90 individuals in a full-sib family, combining 2719 SNP and 84 SSR segregating markers among the parental maps. The consensus SNP and SSR map contains a total of 1201 markers in 23 linkage groups spanning 2008.87 cM, at an average inter-marker distance of 1.67 cM with a minimum logarithm of odds of 6 and maximum recombination fraction of 0.40. Comparisons of the organization the green ash map with the genomes of asterid species coffee and tomato, and genomes of the rosid species poplar and peach, showed areas of conserved gene order, with overall synteny strongest with coffee.
DOI: 10.1007/s11103-018-0815-9
PubMed: 30604323
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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The green ash map shows stronger synteny with coffee than tomato. Green ash (Fraxinus pennsylvanica) is an outcrossing, diploid (2n = 46) hardwood tree species, native to North America. Native ash species in North America are being threatened by the rapid spread of the emerald ash borer (EAB, Agrilus planipennis), an invasive pest from Asia. Green ash, the most widely distributed ash species, is severely affected by EAB infestation, yet few genomic resources for genetic studies and improvement of green ash are available. In this study, a total of 5712 high quality single nucleotide polymorphisms (SNPs) were discovered using a minimum allele frequency of 1% across the entire genome through genotyping-by-sequencing. We also screened hundreds of genomic- and EST-based microsatellite markers (SSRs) from previous de novo assemblies (Staton et al., PLoS ONE 10:e0145031, 2015; Lane et al., BMC Genom 17:702, 2016). A first genetic linkage map of green ash was constructed from 90 individuals in a full-sib family, combining 2719 SNP and 84 SSR segregating markers among the parental maps. The consensus SNP and SSR map contains a total of 1201 markers in 23 linkage groups spanning 2008.87 cM, at an average inter-marker distance of 1.67 cM with a minimum logarithm of odds of 6 and maximum recombination fraction of 0.40. Comparisons of the organization the green ash map with the genomes of asterid species coffee and tomato, and genomes of the rosid species poplar and peach, showed areas of conserved gene order, with overall synteny strongest with coffee.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30604323</PMID><DateCompleted><Year>2019</Year><Month>02</Month><Day>19</Day></DateCompleted><DateRevised><Year>2020</Year><Month>02</Month><Day>25</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1573-5028</ISSN><JournalIssue CitedMedium="Internet"><Volume>99</Volume><Issue>3</Issue><PubDate><Year>2019</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Plant molecular biology</Title><ISOAbbreviation>Plant Mol Biol</ISOAbbreviation></Journal><ArticleTitle>The first genetic linkage map for Fraxinus pennsylvanica and syntenic relationships with four related species.</ArticleTitle><Pagination><MedlinePgn>251-264</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s11103-018-0815-9</ELocationID><Abstract><AbstractText Label="KEY MESSAGE" NlmCategory="UNASSIGNED">The genetic linkage map for green ash (Fraxinus pennsylvanica) contains 1201 DNA markers in 23 linkage groups spanning 2008.87cM. The green ash map shows stronger synteny with coffee than tomato. Green ash (Fraxinus pennsylvanica) is an outcrossing, diploid (2n = 46) hardwood tree species, native to North America. Native ash species in North America are being threatened by the rapid spread of the emerald ash borer (EAB, Agrilus planipennis), an invasive pest from Asia. Green ash, the most widely distributed ash species, is severely affected by EAB infestation, yet few genomic resources for genetic studies and improvement of green ash are available. In this study, a total of 5712 high quality single nucleotide polymorphisms (SNPs) were discovered using a minimum allele frequency of 1% across the entire genome through genotyping-by-sequencing. We also screened hundreds of genomic- and EST-based microsatellite markers (SSRs) from previous de novo assemblies (Staton et al., PLoS ONE 10:e0145031, 2015; Lane et al., BMC Genom 17:702, 2016). A first genetic linkage map of green ash was constructed from 90 individuals in a full-sib family, combining 2719 SNP and 84 SSR segregating markers among the parental maps. The consensus SNP and SSR map contains a total of 1201 markers in 23 linkage groups spanning 2008.87 cM, at an average inter-marker distance of 1.67 cM with a minimum logarithm of odds of 6 and maximum recombination fraction of 0.40. Comparisons of the organization the green ash map with the genomes of asterid species coffee and tomato, and genomes of the rosid species poplar and peach, showed areas of conserved gene order, with overall synteny strongest with coffee.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Di</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Koch</LastName><ForeName>Jennifer</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>USDA Forest Service, Northern Research Station, Project NRS-16, 359 Main Road, Delaware, OH, 43015, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Coggeshall</LastName><ForeName>Mark</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Forestry, Center for Agroforestry, University of Missouri, Columbia, MO, 65211, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>USDA Forest Service, Northern Research Station, Hardwood Tree Improvement and Regeneration Center, Project NRS-14, 715 W. State Street, West Lafayette, IN, 47907, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Carlson</LastName><ForeName>John</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA. jec16@psu.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>IOS-1025974</GrantID><Agency>National Science Foundation (US)</Agency><Country></Country></Grant><Grant><GrantID>PEN04532</GrantID><Agency>USDA National Institute of Food and Agriculture</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>01</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Plant Mol Biol</MedlineTA><NlmUniqueID>9106343</NlmUniqueID><ISSNLinking>0167-4412</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D003069">Coffee</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="Y">Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003069" MajorTopicYN="N">Coffee</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001517" MajorTopicYN="N">Coleoptera</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D031661" MajorTopicYN="N">Fraxinus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005787" MajorTopicYN="N">Gene Frequency</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008040" MajorTopicYN="Y">Genetic Linkage</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D060005" MajorTopicYN="N">Genotyping Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018551" MajorTopicYN="N">Lycopersicon esculentum</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D026801" MajorTopicYN="N">Synteny</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Genotyping-by-sequencing (GBS)</Keyword><Keyword MajorTopicYN="N">Green ash</Keyword><Keyword MajorTopicYN="N">Linkage map</Keyword><Keyword MajorTopicYN="N">Simple sequence repeats (SSRs)</Keyword><Keyword MajorTopicYN="N">Single nucleotide polymorphism (SNP)</Keyword><Keyword MajorTopicYN="N">Synteny</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>08</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>12</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>1</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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sort="Carlson, John" uniqKey="Carlson J" first="John" last="Carlson">John Carlson</name><name sortKey="Coggeshall, Mark" sort="Coggeshall, Mark" uniqKey="Coggeshall M" first="Mark" last="Coggeshall">Mark Coggeshall</name><name sortKey="Coggeshall, Mark" sort="Coggeshall, Mark" uniqKey="Coggeshall M" first="Mark" last="Coggeshall">Mark Coggeshall</name><name sortKey="Koch, Jennifer" sort="Koch, Jennifer" uniqKey="Koch J" first="Jennifer" last="Koch">Jennifer Koch</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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